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- PDB-4zht: Crystal structure of UDP-GlcNAc 2-epimerase -

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Basic information

Entry
Database: PDB / ID: 4zht
TitleCrystal structure of UDP-GlcNAc 2-epimerase
ComponentsBifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
KeywordsISOMERASE / Inhibitor / Complex / Epimerase
Function / homology
Function and homology information


Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism ...Defective GNE causes sialuria, NK and IBM2 / UDP-N-acetylglucosamine 2-epimerase (hydrolysing) / N-acetylglucosamine biosynthetic process / N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylneuraminate biosynthetic process / hexokinase activity / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine metabolic process / Sialic acid metabolism / hydrolase activity, hydrolyzing O-glycosyl compounds / ATP binding / metal ion binding / cytosol
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase,UDP-hydrolysing / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / ROK family / ROK family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-mannopyranose / Chem-NCC / URIDINE-5'-DIPHOSPHATE / Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsChen, S.C. / Yang, C.S. / Ko, T.P. / Chen, Y.
CitationJournal: Sci Rep / Year: 2016
Title: Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis.
Authors: Chen, S.C. / Huang, C.H. / Lai, S.J. / Yang, C.S. / Hsiao, T.H. / Lin, C.H. / Fu, P.K. / Ko, T.P. / Chen, Y.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
B: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
C: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
D: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,59613
Polymers188,3014
Non-polymers4,2969
Water5,963331
1
A: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
B: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules

A: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
B: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,37512
Polymers188,3014
Non-polymers4,0748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area19750 Å2
ΔGint-104 kcal/mol
Surface area49730 Å2
MethodPISA
2
C: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
D: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules

C: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
D: Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,81814
Polymers188,3014
Non-polymers4,51710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20480 Å2
ΔGint-94 kcal/mol
Surface area49470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.041, 98.102, 154.722
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

21B-644-

HOH

31B-662-

HOH

41B-664-

HOH

51C-635-

HOH

61C-648-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A8 - 388
2010B8 - 388
1020A7 - 387
2020C7 - 387
1030A8 - 389
2030D8 - 389
1040B8 - 387
2040C8 - 387
1050B8 - 388
2050D8 - 388
1060C8 - 387
2060D8 - 387

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase / UDP-GlcNAc-2-epimerase/ManAc kinase


Mass: 47075.207 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNE, GLCNE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9Y223, UDP-N-acetylglucosamine 2-epimerase (hydrolysing)
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-NCC / CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID


Mass: 614.451 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H31N4O16P
#4: Sugar ChemComp-BM7 / 2-acetamido-2-deoxy-beta-D-mannopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DManpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-mannopyranosamineCOMMON NAMEGMML 1.0
b-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.1, 19% PEG 3350
PH range: 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. obs: 43536 / % possible obs: 99.8 % / Redundancy: 7.5 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 27.699 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22509 2183 5 %RANDOM
Rwork0.18881 ---
obs0.19061 41334 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.448 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20.74 Å2
2--0.42 Å20 Å2
3----2.49 Å2
Refinement stepCycle: 1 / Resolution: 2.69→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12071 0 279 331 12681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912587
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212234
X-RAY DIFFRACTIONr_angle_refined_deg1.64217034
X-RAY DIFFRACTIONr_angle_other_deg1.405328155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86551528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95723.736554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.096152106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4311588
X-RAY DIFFRACTIONr_chiral_restr0.0880.21957
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213868
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022833
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9744.4016124
X-RAY DIFFRACTIONr_mcbond_other1.9734.4016123
X-RAY DIFFRACTIONr_mcangle_it3.3356.67648
X-RAY DIFFRACTIONr_mcangle_other3.3356.6017649
X-RAY DIFFRACTIONr_scbond_it2.334.7526463
X-RAY DIFFRACTIONr_scbond_other2.334.7526464
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7837.0189387
X-RAY DIFFRACTIONr_long_range_B_refined6.56835.33913387
X-RAY DIFFRACTIONr_long_range_B_other6.55535.29413367
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A491620.07
12B491620.07
21A493360.06
22C493360.06
31A496260.06
32D496260.06
41B492040.06
42C492040.06
51B495000.06
52D495000.06
61C491620.07
62D491620.07
LS refinement shellResolution: 2.694→2.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 151 -
Rwork0.293 2940 -
obs--96.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8026-0.1184-0.79461.15090.08851.9916-0.01610.26780.1219-0.19070.0840.0091-0.32-0.1171-0.06790.6671-0.0541-0.07090.12840.00050.02430.423968.528752.6858
21.99810.0542-0.50141.30660.32841.2272-0.09210.3719-0.2967-0.2066-0.02920.32810.0283-0.50180.12130.4835-0.0488-0.13610.2278-0.04620.1524-31.634850.914566.3786
31.36550.07070.45232.39740.56261.87960.0933-0.0523-0.28490.20040.1798-0.4825-0.29280.2569-0.27320.2117-0.0871-0.02330.1417-0.05190.158215.98938.348513.3363
41.0892-0.12340.44623.37640.29932.32290.4062-0.242-0.39640.93060.03190.07060.4457-0.1476-0.43810.4686-0.1254-0.21270.10760.17510.30470.1063.302120.8672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 390
2X-RAY DIFFRACTION2B8 - 389
3X-RAY DIFFRACTION3C6 - 388
4X-RAY DIFFRACTION4D8 - 390

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